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Research: Genome-wide detection of novel regulatory RNAs in E. coli
- Rahul Raghavan,
- Eduardo A. Groisman,
- and Howard Ochman
Genome Res. September 2011 21: 1487-1497; Published in Advance June 10, 2011, doi:10.1101/gr.119370.110
...Genome-wide detection of novel regulatory RNAs in E. coli Rahul Raghavan 1 , 2 , Eduardo A. Groisman 2 , 3 and Howard Ochman 1 , 2 , 4 1Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06516, USA...
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Research: Genome-wide analysis of promoter architecture in Drosophila melanogaster
- Roger A. Hoskins,
- Jane M. Landolin,
- James B. Brown,
- Jeremy E. Sandler,
- Hazuki Takahashi,
- Timo Lassmann,
- Charles Yu,
- Benjamin W. Booth,
- Dayu Zhang,
- Kenneth H. Wan,
- Li Yang,
- Nathan Boley,
- Justen Andrews,
- Thomas C. Kaufman,
- Brenton R. Graveley,
- Peter J. Bickel,
- Piero Carninci,
- Joseph W. Carlson,
- and Susan E. Celniker
Genome Res. February 2011 21: 182-192; Published in Advance December 22, 2010, doi:10.1101/gr.112466.110
...Genome-wide analysis of promoter architecture in Drosophila melanogaster Roger A. Hoskins 1 , 7 , Jane M. Landolin 1 , 7 , James B. Brown 2 , 7 , Jeremy E. Sandler 1 , Hazuki Takahashi 3 , Timo Lassmann 3 , Charles Yu...
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Research: Genome-wide parent-of-origin DNA methylation analysis reveals the intricacies of human imprinting and suggests a germline methylation-independent mechanism of establishment
- Franck Court,
- Chiharu Tayama,
- Valeria Romanelli,
- Alex Martin-Trujillo,
- Isabel Iglesias-Platas,
- Kohji Okamura,
- Naoko Sugahara,
- Carlos Simón,
- Harry Moore,
- Julie V. Harness,
- Hans Keirstead,
- Jose Vicente Sanchez-Mut,
- Eisuke Kaneki,
- Pablo Lapunzina,
- Hidenobu Soejima,
- Norio Wake,
- Manel Esteller,
- Tsutomu Ogata,
- Kenichiro Hata,
- Kazuhiko Nakabayashi,
- and David Monk
Genome Res. April 2014 24: 554-569; Published in Advance January 8, 2014, doi:10.1101/gr.164913.113
...Genome-wide parent-of-origin DNA methylation analysis reveals the intricacies of human imprinting and suggests a germline methylation-independent mechanism of establishment Franck Court 1 , 15 , Chiharu Tayama 2 , 15 , Valeria Romanelli 1 , 15 , Alex...
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Research: A genome-wide analysis of common fragile sites: What features determine chromosomal instability in the human genome?
- Arkarachai Fungtammasan,
- Erin Walsh,
- Francesca Chiaromonte,
- Kristin A. Eckert,
- and Kateryna D. Makova
Genome Res. June 2012 22: 993-1005; Published in Advance March 28, 2012, doi:10.1101/gr.134395.111
...(2009) discovered that evolutionary breakpoint regions are enriched in structural variants, SNPs, genes, and Genome-wide predictors of common fragile sites Genome Research 1001 www..org pseudogenes, and depleted in recombination hotspots and most conserved elements. The significance of evolutionary...
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Methods: Genome-wide identification of spliced introns using a tiling microarray
- Zhihong Zhang,
- Jay R. Hesselberth,
- and Stanley Fields
Genome Res. April 2007 17: 503-509; Published in Advance March 9, 2007, doi:10.1101/gr.6049107
...-Engele, P. , Kan, Z. , Loerch, P.M. , Armour, C.D. , Santos, R. , Schadt, E.E. , Stoughton, R. , Shoemaker, D.D. ( 2003 ) Genome-wide survey of human alternative pre-mRNA splicing with exon junction microarrays . Science 302 : 2141 – 2144 . ↵ Kampa, D. , Cheng, J. , Kapranov, P. , Yamanaka, M. , Brubaker, S...
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Methods: Enredo and Pecan: Genome-wide mammalian consistency-based multiple alignment with paralogs
- Benedict Paten,
- Javier Herrero,
- Kathryn Beal,
- Stephen Fitzgerald,
- and Ewan Birney
Genome Res. November 2008 18: 1814-1828; Published in Advance October 10, 2008, doi:10.1101/gr.076554.108
...Enredo and Pecan: Genome-wide mammalian consistency-based multiple alignment with paralogs Benedict Paten 1 , 3 , 4 , Javier Herrero 2 , 3 , Kathryn Beal 2 , Stephen Fitzgerald 2 , and Ewan Birney 2 , 4 1 Center...
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RESOURCE: Genome-wide assembly and analysis of alternative transcripts in mouse
- Alexei A. Sharov,
- Dawood B. Dudekula,
- and Minoru S.H. Ko
Genome Res. May 2005 15: 748-754; doi:10.1101/gr.3269805
....D., Santos, R., Schadt, E.E., Stoughton, R., and Shoemaker, D.D. 2003 . Genome-wide survey of human alternative pre-mRNA splicing with exon junction microarrays. Science 302 : 2141 –2144. ↵ Kan, Z., Rouchka, E.C., Gish, W.R., and States, D.J. 2001 . Gene structure prediction and alternative splicing analysis...
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PERSPECTIVE: Genome-wide analyses of alternative splicing in plants: Opportunities and challenges
- W. Brad Barbazuk,
- Yan Fu,
- and Karen M. McGinnis
Genome Res. September 2008 18: 1381-1392; Published in Advance July 30, 2008, doi:10.1101/gr.053678.106
...Genome-wide analyses of alternative splicing in plants: Opportunities and challenges W. Brad Barbazuk 1 , 3 , 4 , Yan Fu 1 , and Karen M. McGinnis 2 1 Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA; 2...
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LETTER: Ubiquitous selective constraints in the Drosophila genome revealed by a genome-wide interspecies comparison
- Daniel L. Halligan and
- Peter D. Keightley
Genome Res. July 2006 16: 875-884; Published in Advance June 2, 2006, doi:10.1101/gr.5022906
...Ubiquitous selective constraints in the Drosophila genome revealed by a genome-wide interspecies comparison Daniel L. Halligan 1 and Peter D. Keightley Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom...
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Research: Genome-wide mapping of nuclear mitochondrial DNA sequences links DNA replication origins to chromosomal double-strand break formation in Schizosaccharomyces pombe
- Sandrine Lenglez,
- Damien Hermand,
- and Anabelle Decottignies
Genome Res. September 2010 20: 1250-1261; Published in Advance August 5, 2010, doi:10.1101/gr.104513.109
...Genome-wide mapping of nuclear mitochondrial DNA sequences links DNA replication origins to chromosomal double-strand break formation in Schizosaccharomyces pombe Sandrine Lenglez 1 , Damien Hermand 2 and Anabelle Decottignies 1 , 3 1 Catholic...

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